P322: DECIPHERING THE UNDERLYING MOLECULAR COMPLEXITY OF THE IKZF1PLUS SIGNATURE
Authors: Jonathan Lühmann, Winfried Hofmann, Anke Katharina Bergmann, Anja Möricke, Gunnar Cario, Martin Schrappe, Brigitte Schlegelberger, Martin Zimmermann, Martin Stanulla, Doris Steinemann
Journal: HemaSphere (2023)

Background: Acute lymphoblastic leukemia (ALL) is the most frequent pediatric cancer. Even though novel therapeutic strategies and stratification led to a ~90% long-term cure, there is still a proportion of patients experiencing relapse or therapy-related toxicities. Recently, the IKZF1plus profile, defined as the presence of a deletion in IKZF1 together with one or more additional deletions in PAX5 and/or CDKN2A/B and/or PAR1 and the absence of a deletion in ERG, was characterized as a very poor prognostic marker specifically in MRD-positive patients based on retrospective analyses of the AIEOP-BFM ALL 2000/2009 trials (PMID 29498923). Dependent on MRD at day 33, IKZF1plus is used for high-risk stratification in the ongoing AIEOP-BFM ALL 2017 trial. Aims: This retrospective study aimed to decipher the underlying molecular complexity of the IKZF1plus profile by reanalyzing patients from the AIEOP-BFM ALL 2000 and 2009 trials with optical genome mapping (OGM), a molecular cytogenetic approach which allows the parallel detection of all kinds of structural variants including copy number variations, translocation as well as aneuploidies. Methods: In total, 142 patients with IKZF1 deletion (73 with IKZF1del, 69 with IKZF1plus profile) as determined by MLPA in previous analyses were re-analyzed by means of OGM. Based on our findings seven patients were not eligible and eight patients were reclassified from IKZF1del to IKZF1plus or vice versa (94.1% concordance with MLPA). Results were validated by comparison to previously collected data and in case of new fusions by RT-PCR/RNA-Seq. Next, genetic markers were correlated with patient outcome (5-year event-free survival (EFS), overall survival and cumulative incidence of relapse). Results: In 45.9% of the analyzed patients either known prognostic markers (18/135; 13.3% with ETV6::RUNX1, high hyperdiploidy or iAMP21) or other gene fusions (44/135; 32.6%) were identified. These fusions were evenly distributed among the subgroups (21 IKZF1del and 23 IKZF1del) and categorized into: ABL-class fusions (12; 8.9%), PAX5 fusions (9; 6.7%), JAK2 fusions (10; 7.4%), ZNF384 fusions (4; 3.0%) and other fusions (9; 6.7%). Investigating the patient outcome, we reproduced the initial results (PMID 29498923) and show that IKZF1del and especially IKZF1plus positives did much worse compared to a cohort 845 other patients from the AIEOP-BFM ALL 2000 and 2009 trials without an IKZF1 deletion (EFS 73.1±5.3 vs 60.6±6.3 vs 87.1±1.2). The dismal outcome was even more pronounced when we excluded patients with an established good prognostic marker from both groups. (EFS IKZF1del vs IKZF1plus; 68.3±6.2 vs 62.0±6.4). IKZF1-deleted patients with a favorable prognostic marker (high hyperdiploidy and ETV6::RUNX1) had an EFS of 100% and were exclusively found in the IKZF1del but not the IKZF1plus subgroup. Furthermore, IKZF1del/plus patients had an inferior 5-year EFS in the presence of a gene fusion (55.9±7.6), especially with ABL-class (41.7±14.2), JAK2 (60.0±15.5) and PAX5 (50.0±17.7) fusions when compared to the absence of fusions (70.5±5.4). Validation of our results in an independent cohort is ongoing. Summary/Conclusion: By using OGM, we show that the genomic landscape in ALL is complex and that ~46% of the IKZF1del/plus patients carry an established marker or other gene fusions which may be the underlying leukemogenic driver and contribute to an (un-) favorable outcome. Thus, a comprehensive genetic characterization could be valuable to further improve risk-adapted treatment stratification. Keywords: Acute lymphoblastic leukemia, Gene fusion, Ikaros, Pediatric